Personally I like the pre-solo riff in 'The Leper Affinity'. A multitude of riffs from the track 'Blackwater Park' and the first heavy riff in 'The Moor'. Oh yeah, can't forget the first two in Demon of the Fall.
Actually I've thought for a while that 3:16 of 'Serenity Painted Death' is Opeth's best riff ever. That shit is a total composite... it's like the backing part was made up of entirely random ideas that work in perfect cohesion. Not only that but he puts a fuckin lead over it! wtf?/!!one!1!1